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comparison gemini_annotate.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children ce61d4876838
comparison
equal deleted inserted replaced
16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>adding your own custom annotations</description> 2 <description>adding your own custom annotations</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">annotate</token> 5 <token name="@BINARY@">annotate</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 12
12 bgzip -c $annotate_source > tabixed.gz; 13 bgzip -c $annotate_source > tabixed.gz;
13 tabix -p bed tabixed.gz; 14 tabix -p bed tabixed.gz;
25 "${ infile }" 26 "${ infile }"
26 > "${ outfile }" 27 > "${ outfile }"
27 ]]> 28 ]]>
28 29
29 </command> 30 </command>
30 <expand macro="stdio" />
31 <inputs> 31 <inputs>
32 <expand macro="infile" /> 32 <expand macro="infile" />
33 <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/> 33 <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
34 34
35 <param name="column_name" size="20" type="text" value="" 35 <param name="column_name" size="20" type="text" value=""
36 label="The name of the column to be added to the variant table" help="(-c)"> 36 label="The name of the column to be added to the variant table" help="(-c)">
37 <sanitizer invalid_char=" "> 37 <sanitizer invalid_char=" ">
38 <valid initial="string.letters,string.digits"> 38 <valid initial="string.letters,string.digits">
39 <add value="_" /> 39 <add value="_" />
40 </valid> 40 </valid>
41 </sanitizer> 41 </sanitizer>
42 </param> 42 </param>
43 <conditional name="a"> 43 <conditional name="a">
44 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)"> 44 <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
46 <option value="count">How many regions did a variant overlap? (count)</option> 46 <option value="count">How many regions did a variant overlap? (count)</option>
47 <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option> 47 <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option>
48 </param> 48 </param>
49 <when value="extract"> 49 <when value="extract">
50 50
51 <param name="column_extracts" label="Column to extract information from for list annotations" 51 <param name="column_extracts" label="Column to extract information from for list annotations"
52 type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/> 52 type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/>
53 53
54 54
55 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?" 55 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
56 help="(-t)"> 56 help="(-t)">